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CHECK report for SC3 on tokay1

This page was generated on 2018-04-12 13:27:21 -0400 (Thu, 12 Apr 2018).

Package 1250/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SC3 1.7.7
Vladimir Kiselev
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/SC3
Branch: RELEASE_3_6
Last Commit: 860f8e5
Last Changed Date: 2018-01-25 06:08:07 -0400 (Thu, 25 Jan 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SC3
Version: 1.7.7
Command: rm -rf SC3.buildbin-libdir SC3.Rcheck && mkdir SC3.buildbin-libdir SC3.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SC3.buildbin-libdir SC3_1.7.7.tar.gz >SC3.Rcheck\00install.out 2>&1 && cp SC3.Rcheck\00install.out SC3-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SC3.buildbin-libdir --install="check:SC3-install.out" --force-multiarch --no-vignettes --timings SC3_1.7.7.tar.gz
StartedAt: 2018-04-12 02:59:30 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 03:03:45 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 255.7 seconds
RetCode: 0
Status:  OK  
CheckDir: SC3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SC3.buildbin-libdir SC3.Rcheck && mkdir SC3.buildbin-libdir SC3.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SC3.buildbin-libdir SC3_1.7.7.tar.gz >SC3.Rcheck\00install.out 2>&1 && cp SC3.Rcheck\00install.out SC3-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SC3.buildbin-libdir --install="check:SC3-install.out" --force-multiarch --no-vignettes --timings SC3_1.7.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/SC3.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SC3/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SC3' version '1.7.7'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'SC3' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.2Mb
    libs   1.5Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/SC3.buildbin-libdir/SC3/libs/i386/SC3.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/SC3.Rcheck/00check.log'
for details.



Installation output

SC3.Rcheck/00install.out


install for i386

* installing *source* package 'SC3' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c cppFunctions.cpp -o cppFunctions.o
cppFunctions.cpp: In function 'arma::mat consmx(arma::mat)':
cppFunctions.cpp:63:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < dat.n_cols; j++) {
                ^
cppFunctions.cpp:64:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < dat.n_rows; i++) {
                 ^
cppFunctions.cpp:65:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (k = i + 1; k < dat.n_rows; k++) {
                      ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o SC3.dll tmp.def RcppExports.o cppFunctions.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/SC3.buildbin-libdir/SC3/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'SC3'
    finding HTML links ... done
    ED1                                     html  
    ED2                                     html  
    ann                                     html  
    calculate_distance                      html  
    calculate_stability                     html  
    consensus_matrix                        html  
    consmx                                  html  
    estkTW                                  html  
    get_auroc                               html  
    get_biolgy                              html  
    get_de_genes                            html  
    get_marker_genes                        html  
    get_outl_cells                          html  
    get_processed_dataset                   html  
    markers_for_heatmap                     html  
    norm_laplacian                          html  
    organise_de_genes                       html  
    organise_marker_genes                   html  
    prepare_for_svm                         html  
    reindex_clusters                        html  
    sc3                                     html  
    sc3_calc_biology                        html  
    sc3_calc_consens                        html  
    sc3_calc_dists                          html  
    sc3_calc_transfs                        html  
    sc3_estimate_k                          html  
    sc3_export_results_xls                  html  
    sc3_interactive                         html  
    sc3_kmeans                              html  
    sc3_plot_cluster_stability              html  
    sc3_plot_consensus                      html  
    sc3_plot_de_genes                       html  
    sc3_plot_expression                     html  
    sc3_plot_markers                        html  
    sc3_plot_silhouette                     html  
    sc3_prepare                             html  
    sc3_run_svm                             html  
    support_vector_machines                 html  
    tmult                                   html  
    transformation                          html  
    yan                                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'SC3' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c cppFunctions.cpp -o cppFunctions.o
cppFunctions.cpp: In function 'arma::mat consmx(arma::mat)':
cppFunctions.cpp:63:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < dat.n_cols; j++) {
                ^
cppFunctions.cpp:64:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < dat.n_rows; i++) {
                 ^
cppFunctions.cpp:65:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (k = i + 1; k < dat.n_rows; k++) {
                      ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o SC3.dll tmp.def RcppExports.o cppFunctions.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/SC3.buildbin-libdir/SC3/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SC3' as SC3_1.7.7.zip
* DONE (SC3)
In R CMD INSTALL
In R CMD INSTALL

Tests output


Example timings

SC3.Rcheck/examples_i386/SC3-Ex.timings

nameusersystemelapsed
get_de_genes0.750.070.81
get_marker_genes0.220.040.27
get_outl_cells0.330.020.34
reindex_clusters000

SC3.Rcheck/examples_x64/SC3-Ex.timings

nameusersystemelapsed
get_de_genes1.380.021.39
get_marker_genes0.300.020.31
get_outl_cells0.470.030.50
reindex_clusters000